1##fileformat=VCFv4.2 2##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> 3##FILTER=<ID=LowQual,Description="Low quality"> 4##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> 5##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> 6##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> 7##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 8##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> 9##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> 10##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> 11##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> 12##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> 13##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.7-43-gc7dbd4f,Date="Tue Jun 27 08:40:17 EDT 2017",Epoch=1498567217692,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37_decoy.NA12892.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[20:10433000-10437000, 20:10087820, 20:10684106] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, AS_Standard] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> 14##GVCFBlock0-20=minGQ=0(inclusive),maxGQ=20(exclusive) 15##GVCFBlock20-100=minGQ=20(inclusive),maxGQ=100(exclusive) 16##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> 17##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> 18##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> 19##INFO=<ID=AS_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities"> 20##INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele"> 21##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> 22##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="allele specific heterozygosity as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation; relate to inbreeding coefficient"> 23##INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality"> 24##INFO=<ID=AS_MQRankSum,Number=A,Type=Float,Description="Allele-specific Mapping Quality Rank Sum"> 25##INFO=<ID=AS_QD,Number=A,Type=Float,Description="Allele-specific Variant Confidence/Quality by Depth"> 26##INFO=<ID=AS_QUALapprox,Number=1,Type=String,Description="Allele-specific QUAL approximations"> 27##INFO=<ID=AS_RAW_BaseQRankSum,Number=1,Type=String,Description="raw data for allele specific rank sum test of base qualities"> 28##INFO=<ID=AS_RAW_MQ,Number=A,Type=Float,Description="Allele-specfic raw data for RMS Mapping Quality"> 29##INFO=<ID=AS_RAW_MQRankSum,Number=1,Type=String,Description="Allele-specific raw data for Mapping Quality Rank Sum"> 30##INFO=<ID=AS_RAW_ReadPosRankSum,Number=1,Type=String,Description="allele specific raw data for rank sum test of read position bias"> 31##INFO=<ID=AS_ReadPosRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref read position bias"> 32##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests"> 33##INFO=<ID=AS_SOR,Number=A,Type=Float,Description="Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias"> 34##INFO=<ID=AS_VarDP,Number=1,Type=String,Description="Allele-specific (informative) depth over variant genotypes -- including ref, RAW format"> 35##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> 36##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> 37##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> 38##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> 39##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> 40##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> 41##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> 42##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 43##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> 44##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead.)"> 45##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> 46##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score"> 47##INFO=<ID=RAW_GT_COUNT,Number=3,Type=Integer,Description="Counts of genotypes w.r.t. the reference allele: 0/0, 0/*, */*, i.e. all alts lumped together; for use in calculating excess heterozygosity"> 48##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality (deprecated -- use RAW_MQandDP instead.)"> 49##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation."> 50##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> 51##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> 52##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes"> 53##contig=<ID=1,length=249250621> 54##contig=<ID=2,length=243199373> 55##contig=<ID=3,length=198022430> 56##contig=<ID=4,length=191154276> 57##contig=<ID=5,length=180915260> 58##contig=<ID=6,length=171115067> 59##contig=<ID=7,length=159138663> 60##contig=<ID=8,length=146364022> 61##contig=<ID=9,length=141213431> 62##contig=<ID=10,length=135534747> 63##contig=<ID=11,length=135006516> 64##contig=<ID=12,length=133851895> 65##contig=<ID=13,length=115169878> 66##contig=<ID=14,length=107349540> 67##contig=<ID=15,length=102531392> 68##contig=<ID=16,length=90354753> 69##contig=<ID=17,length=81195210> 70##contig=<ID=18,length=78077248> 71##contig=<ID=19,length=59128983> 72##contig=<ID=20,length=63025520> 73##contig=<ID=21,length=48129895> 74##contig=<ID=22,length=51304566> 75##contig=<ID=X,length=155270560> 76##contig=<ID=Y,length=59373566> 77##contig=<ID=MT,length=16569> 78##contig=<ID=GL000207.1,length=4262> 79##contig=<ID=GL000226.1,length=15008> 80##contig=<ID=GL000229.1,length=19913> 81##contig=<ID=GL000231.1,length=27386> 82##contig=<ID=GL000210.1,length=27682> 83##contig=<ID=GL000239.1,length=33824> 84##contig=<ID=GL000235.1,length=34474> 85##contig=<ID=GL000201.1,length=36148> 86##contig=<ID=GL000247.1,length=36422> 87##contig=<ID=GL000245.1,length=36651> 88##contig=<ID=GL000197.1,length=37175> 89##contig=<ID=GL000203.1,length=37498> 90##contig=<ID=GL000246.1,length=38154> 91##contig=<ID=GL000249.1,length=38502> 92##contig=<ID=GL000196.1,length=38914> 93##contig=<ID=GL000248.1,length=39786> 94##contig=<ID=GL000244.1,length=39929> 95##contig=<ID=GL000238.1,length=39939> 96##contig=<ID=GL000202.1,length=40103> 97##contig=<ID=GL000234.1,length=40531> 98##contig=<ID=GL000232.1,length=40652> 99##contig=<ID=GL000206.1,length=41001> 100##contig=<ID=GL000240.1,length=41933> 101##contig=<ID=GL000236.1,length=41934> 102##contig=<ID=GL000241.1,length=42152> 103##contig=<ID=GL000243.1,length=43341> 104##contig=<ID=GL000242.1,length=43523> 105##contig=<ID=GL000230.1,length=43691> 106##contig=<ID=GL000237.1,length=45867> 107##contig=<ID=GL000233.1,length=45941> 108##contig=<ID=GL000204.1,length=81310> 109##contig=<ID=GL000198.1,length=90085> 110##contig=<ID=GL000208.1,length=92689> 111##contig=<ID=GL000191.1,length=106433> 112##contig=<ID=GL000227.1,length=128374> 113##contig=<ID=GL000228.1,length=129120> 114##contig=<ID=GL000214.1,length=137718> 115##contig=<ID=GL000221.1,length=155397> 116##contig=<ID=GL000209.1,length=159169> 117##contig=<ID=GL000218.1,length=161147> 118##contig=<ID=GL000220.1,length=161802> 119##contig=<ID=GL000213.1,length=164239> 120##contig=<ID=GL000211.1,length=166566> 121##contig=<ID=GL000199.1,length=169874> 122##contig=<ID=GL000217.1,length=172149> 123##contig=<ID=GL000216.1,length=172294> 124##contig=<ID=GL000215.1,length=172545> 125##contig=<ID=GL000205.1,length=174588> 126##contig=<ID=GL000219.1,length=179198> 127##contig=<ID=GL000224.1,length=179693> 128##contig=<ID=GL000223.1,length=180455> 129##contig=<ID=GL000195.1,length=182896> 130##contig=<ID=GL000212.1,length=186858> 131##contig=<ID=GL000222.1,length=186861> 132##contig=<ID=GL000200.1,length=187035> 133##contig=<ID=GL000193.1,length=189789> 134##contig=<ID=GL000194.1,length=191469> 135##contig=<ID=GL000225.1,length=211173> 136##contig=<ID=GL000192.1,length=547496> 137##contig=<ID=NC_007605,length=171823> 138##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta 139#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12892 14020 10087820 . C CAGAGAG,<NON_REF> 598.60 . AS_QUALapprox=|606|0;AS_RAW_BaseQRankSum=|1.0,1|NaN;AS_RAW_MQ=97208.00|47258.00|0.00;AS_RAW_MQRankSum=|-3.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=16,13|12,12|0,0;AS_VarDP=29|24|0;BaseQRankSum=0.955;DP=74;MQRankSum=-3.130;MQ_DP=74;QUALapprox=606;RAW_GT_COUNT=0,1,0;RAW_MQ=211789.00;RAW_MQandDP=211789,74;ReadPosRankSum=-0.254;VarDP=55 GT:AD:GQ:PL:SB 0/1:29,24,0:99:606,0,849,697,927,1653:16,13,12,14 14120 10433000 . G <NON_REF> . . END=10433308 GT:DP:GQ:MIN_DP:PL 0/0:37:21:29:0,21,315 14220 10433309 . T <NON_REF> . . END=10433319 GT:DP:GQ:MIN_DP:PL 0/0:30:6:25:0,6,90 14320 10433321 . A <NON_REF> . . END=10433321 GT:DP:GQ:MIN_DP:PL 0/0:35:21:35:0,21,315 14420 10433322 . A AT,<NON_REF> 442.60 . AS_QUALapprox=|450|0;AS_RAW_BaseQRankSum=|0.8,1|NaN;AS_RAW_MQ=3364.00|31589.00|0.00;AS_RAW_MQRankSum=|2.2,1|NaN;AS_RAW_ReadPosRankSum=|1.9,1|NaN;AS_SB_TABLE=2,2|6,6|0,0;AS_VarDP=4|12|0;BaseQRankSum=0.877;DP=42;MQRankSum=1.895;MQ_DP=42;QUALapprox=450;RAW_GT_COUNT=0,1,0;RAW_MQ=86818.00;RAW_MQandDP=86818,42;ReadPosRankSum=1.704;VarDP=19 GT:AD:GQ:PL:SB 0/1:4,12,0:46:450,0,46,442,117,617:2,2,8,7 14520 10433324 . A T,<NON_REF> 863.06 . AS_QUALapprox=|877|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=841.00|38317.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,1|11,9|0,0;AS_VarDP=1|20|0;BaseQRankSum=1.458;DP=40;MQRankSum=0.871;MQ_DP=40;QUALapprox=877;RAW_GT_COUNT=0,0,1;RAW_MQ=79618.00;RAW_MQandDP=79618,40;ReadPosRankSum=1.736;VarDP=21 GT:AD:GQ:PGT:PID:PL:SB 1/1:1,20,0:53:0|1:10433324_A_T:877,53,0,880,61,888:0,1,11,9 14620 10433325 . A <NON_REF> . . END=10433325 GT:DP:GQ:MIN_DP:PL 0/0:33:24:33:0,24,1136 14720 10433326 . A T,<NON_REF> 863.06 . AS_QUALapprox=|877|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=841.00|38317.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,1|11,9|0,0;AS_VarDP=1|20|0;BaseQRankSum=1.537;DP=36;MQRankSum=0.871;MQ_DP=36;QUALapprox=877;RAW_GT_COUNT=0,0,1;RAW_MQ=65218.00;RAW_MQandDP=65218,36;ReadPosRankSum=1.736;VarDP=21 GT:AD:GQ:PGT:PID:PL:SB 1/1:1,20,0:53:0|1:10433324_A_T:877,53,0,881,61,888:0,1,11,9 14820 10433327 . A <NON_REF> . . END=10433327 GT:DP:GQ:MIN_DP:PL 0/0:32:23:32:0,23,1108 14920 10433328 . A T,<NON_REF> 1177.06 . AS_QUALapprox=|1191|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|38317.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|11,9|0,0;AS_VarDP=0|20|0;DP=36;MQ_DP=36;QUALapprox=1191;RAW_GT_COUNT=0,0,1;RAW_MQ=65218.00;RAW_MQandDP=65218,36;VarDP=20 GT:AD:GQ:PL:SB 1/1:0,20,0:74:1191,74,0,1132,93,1376:0,0,11,9 15020 10433329 . A <NON_REF> . . END=10433344 GT:DP:GQ:MIN_DP:PL 0/0:37:23:32:0,23,1035 15120 10433346 . T <NON_REF> . . END=10433347 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1260 15220 10433349 . A <NON_REF> . . END=10433350 GT:DP:GQ:MIN_DP:PL 0/0:39:84:39:0,84,1260 15320 10433351 . T <NON_REF> . . END=10433351 GT:DP:GQ:MIN_DP:PL 0/0:37:4:37:0,4,1155 15420 10433353 . G <NON_REF> . . END=10436226 GT:DP:GQ:MIN_DP:PL 0/0:36:27:25:0,27,882 15520 10436227 . T TTTTA,<NON_REF> 411.02 . AS_QUALapprox=|425|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|29194.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|7,3|0,0;AS_VarDP=0|10|0;DP=33;MQ_DP=33;QUALapprox=425;RAW_GT_COUNT=0,0,1;RAW_MQ=111994.00;RAW_MQandDP=111994,33;VarDP=10 GT:AD:GQ:PL:SB 1/1:0,10,0:29:425,29,0,427,30,428:0,0,7,3 15620 10436229 . T <NON_REF> . . END=10437000 GT:DP:GQ:MIN_DP:PL 0/0:33:30:24:0,30,450 15720 10684106 . C <NON_REF> . . END=10684106 GT:DP:GQ:MIN_DP:PL 0/0:46:99:46:0,108,1620 158